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Get core phenotype terms from OncoTree

Source: R/get_tree.R
get_tree.Rd

Downloads and returns a dataset with curated phenotype terms (UMLS) from OncoTree. The dataset comes as a list object, with two elements:

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a data frame with phenotype terms

Usage

get_tree(
  cache_dir = NA,
  force_download = FALSE,
  site = NA,
  max_tree_depth = 6,
  ignore_minor_type = FALSE
)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

site

limit OncoTree terms to those relevant for a given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla of Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head and Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', 'Other/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina'

max_tree_depth

consider only terms up to a given depth in the OncoTree (integer from 1-6, default: 6)

ignore_minor_type

logical indicating if minor tumor types should be excluded or not

Value

metadata - A data frame with 1 row and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used

  • abbreviation - abbreviation used in column names of records

records - A data frame with the following columns:

  • primary_site - Primary tumor type/site

  • ot_main_type - Main tumor type (OncoTree)

  • ot_name - Phenotype name (OncoTree)

  • ot_level - Tree level (OncoTree)

  • ot_code - Phenotype code (OncoTree)

  • ot_code_path - Tree code path (OncoTree)

  • cui - Concept unique identifier (UMLS)

  • cui_name - Phenotype name (UMLS)

  • minor_type - logical indicating whether the term is part of a minor tumor type/site

  • source - term indicating the dataset source

Examples


if (FALSE) { # \dontrun{
library(phenOncoX)
oncology_terms <- get_tree(cache_dir = tempdir())
} # }